Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/GeneTrackToWig.xml @ 24:a77e126ae856 draft
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| author | timpalpant |
|---|---|
| date | Tue, 19 Jun 2012 22:15:09 -0400 |
| parents | 9d56b5b85740 |
| children | b43c420a6135 |
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| 23:01d5d20eaadd | 24:a77e126ae856 |
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| 1 <tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0"> | |
| 2 <description>converter</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="tabular" label="Input GeneTrack index" /> | |
| 6 <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" /> | |
| 7 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" /> | |
| 8 </inputs> | |
| 9 <outputs> | |
| 10 <data name="output" format="wig" metadata_source="input" /> | |
| 11 </outputs> | |
| 12 <tests> | |
| 13 <test> | |
| 14 <param name="input" value="test.genetrack" ftype="tabular"/> | |
| 15 <param name="shift" value="73"/> | |
| 16 <param name="zero" value="true"/> | |
| 17 <param name="chromInfo" value="sacCer2"/> | |
| 18 <output name="output" file="geneTrackToWig1.wig"/> | |
| 19 </test> | |
| 20 <test> | |
| 21 <param name="input" value="test.genetrack" ftype="tabular"/> | |
| 22 <param name="shift" value="0"/> | |
| 23 <param name="zero" value="false"/> | |
| 24 <param name="chromInfo" value="sacCer2"/> | |
| 25 <output name="output" file="geneTrackToWig2.wig"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help> | |
| 29 | |
| 30 This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them. | |
| 31 | |
| 32 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html | |
| 33 | |
| 34 .. class:: warningmark | |
| 35 | |
| 36 This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset. | |
| 37 | |
| 38 </help> | |
| 39 </tool> |